def validate(self):
errors = []
mdIn = mdFirstRow(self.InputFile)
if not mdIn.containsLabel(str2Label(self.InputFileLabel)):
errors.append(self.InputFile + " does not contain the label " + self.InputFileLabel)
mdSubset = mdFirstRow(self.SubsetFile)
if not mdSubset.containsLabel(str2Label(self.SubsetFileLabel)):
errors.append(self.SubsetFile+" does not contain the label " + sself.SubsetFileLabel)
return errors
def run(self):
from xmipp import MetaData, str2Label
from protlib_gui_figure import XmippPlotter
md = MetaData(self.getParam('-i'))
if self.checkParam('--xlabel'):
xlabel = self.getParam('--xlabel')
mdLabelX = str2Label(xlabel)
else:
xlabel = ""
mdLabelX = None
if self.checkParam('--xtitle'):
xlabel = self.getParam('--xtitle')
ylabels = self.getParam('--ylabel').split()
if self.checkParam('--ytitle'):
ylabel = self.getParam('--ytitle')
else:
ylabel = ylabels[0]
colors, lenColors = self.getList('--colors',
['g', 'b', 'r', 'y', 'c', 'm', 'k'])
markers, lenMarkers = self.getList('--markers')
styles, lenStyles = self.getList('--style')
if self.checkParam('--nbins'):
nBins = self.getIntParam('--nbins')
else:
nBins = None
title = self.getParam('--title')
xplotter = XmippPlotter()
xplotter.createSubPlot(title, xlabel, ylabel)
for i, l in enumerate(ylabels):
c = colors[i % lenColors]
m = markers[i % lenMarkers]
if m == "none":
m = None
s = styles[i % lenStyles]
if s == "none":
s = None
xplotter.plotMd(md,
mdLabelX,
str2Label(l),
color=c,
marker=m,
linestyle=s,
nbins=nBins) # if nbins is present do an histogram
legendLocation = self.getParam('--legend')
if legendLocation != 'none':
xplotter.showLegend(ylabels, loc=legendLocation.replace('_', ' '))
xplotter.show()
def createSubset(log, inputFile, inputFileLabel, subsetFile, subsetFileLabel, outputFile):
mdInputFile = MetaData(inputFile)
mdSubsetFile = MetaData(subsetFile)
mdOutputFile = MetaData()
print inputFile, inputFileLabel, subsetFile, subsetFileLabel, outputFile
mdOutputFile.join2( mdInputFile
, mdSubsetFile
, str2Label(inputFileLabel)
, str2Label(subsetFileLabel)
, INNER_JOIN)
mdOutputFile.write(outputFile)
def run(self):
from xmipp import MetaData, str2Label
from protlib_gui_figure import XmippPlotter
md = MetaData(self.getParam('-i'))
if self.checkParam('--xlabel'):
xlabel = self.getParam('--xlabel')
mdLabelX = str2Label(xlabel)
else:
xlabel = ""
mdLabelX = None
if self.checkParam('--xtitle'):
xlabel = self.getParam('--xtitle')
ylabels = self.getParam('--ylabel').split()
if self.checkParam('--ytitle'):
ylabel = self.getParam('--ytitle')
else:
ylabel = ylabels[0]
colors, lenColors = self.getList('--colors', ['g', 'b', 'r', 'y', 'c', 'm', 'k'])
markers, lenMarkers = self.getList('--markers')
styles, lenStyles = self.getList('--style')
if self.checkParam('--nbins'):
nBins = self.getIntParam('--nbins')
else:
nBins = None
title = self.getParam('--title')
xplotter = XmippPlotter()
xplotter.createSubPlot(title, xlabel, ylabel)
for i, l in enumerate(ylabels):
c = colors[i % lenColors]
m = markers[i % lenMarkers]
if m == "none":
m = None
s = styles[i % lenStyles]
if s == "none":
s = None
xplotter.plotMd(md, mdLabelX, str2Label(l), color=c, marker=m, linestyle=s, nbins=nBins)#if nbins is present do an histogram
legendLocation = self.getParam('--legend')
if legendLocation != 'none':
xplotter.showLegend(ylabels, loc=legendLocation.replace('_', ' '))
xplotter.show()
def createMetaDataFromPattern(pattern, isStack=False, label="image"):
''' Create a metadata from files matching pattern'''
import glob
files = glob.glob(pattern)
files.sort()
label = xmipp.str2Label(label) #Check for label value
mD = xmipp.MetaData()
inFile = xmipp.FileName()
nSize = 1
for file in files:
fileAux = file
if isStack:
if file.endswith(".mrc"):
fileAux = file + ":mrcs"
x, x, x, nSize = xmipp.getImageSize(fileAux)
if nSize != 1:
counter = 1
for jj in range(nSize):
inFile.compose(counter, fileAux)
objId = mD.addObject()
mD.setValue(label, inFile, objId)
mD.setValue(xmipp.MDL_ENABLED, 1, objId)
counter += 1
else:
objId = mD.addObject()
mD.setValue(label, fileAux, objId)
mD.setValue(xmipp.MDL_ENABLED, 1, objId)
return mD
def setValue(self, label, value):
"""args: this list should contains tuples with
MetaData Label and the desired value"""
# Allow setValue using the label string
if isinstance(label, basestring):
label = xmipp.str2Label(label)
self._labelDict[label] = value
def setValue(self, label, value):
"""args: this list should contains tuples with
MetaData Label and the desired value"""
# Allow setValue using the label string
if isinstance(label, basestring):
label = str2Label(label)
self._labelDict[label] = value
def createMetaDataFromPattern(pattern, isStack=False, label="image"):
''' Create a metadata from files matching pattern'''
import glob
files = glob.glob(pattern)
files.sort()
from xmipp import MetaData, FileName, getImageSize, MDL_ENABLED, str2Label
label = str2Label(label) #Check for label value
mD = MetaData()
inFile = FileName()
nSize = 1
for file in files:
fileAux=file
if isStack:
if file.endswith(".mrc"):
fileAux=file+":mrcs"
x, x, x, nSize = getImageSize(fileAux)
if nSize != 1:
counter = 1
for jj in range(nSize):
inFile.compose(counter, fileAux)
objId = mD.addObject()
mD.setValue(label, inFile, objId)
mD.setValue(MDL_ENABLED, 1, objId)
counter += 1
else:
objId = mD.addObject()
mD.setValue(label, fileAux, objId)
mD.setValue(MDL_ENABLED, 1, objId)
return mD
def _convertTableToMd(self, table):
colLabels = [(col.getName(), xmipp.str2Label(col.getName())) for col in table.iterColumns()]
md = xmipp.MetaData()
for row in table.iterRows():
objId = md.addObject()
for col, label in colLabels:
if col != "id":
value = getattr(row, col)
md.setValue(label, value, objId)
return md
def _convertTableToMd(self, table):
colLabels = [(col.getName(), xmipp.str2Label(col.getName()))
for col in table.iterColumns()]
md = xmipp.MetaData()
for row in table.iterRows():
objId = md.addObject()
for col, label in colLabels:
if col != 'id':
value = getattr(row, col)
md.setValue(label, value, objId)
return md
def getValue(self, label, default=None):
""" Return the value of the row for a given label. """
# Allow getValue using the label string
if isinstance(label, basestring):
label = xmipp.str2Label(label)
return self._labelDict.get(label, default)
def containsLabel(self, label):
# Allow getValue using the label string
if isinstance(label, basestring):
label = xmipp.str2Label(label)
return label in self._labelDict
def getValue(self, label, default=None):
""" Return the value of the row for a given label. """
# Allow getValue using the label string
if isinstance(label, basestring):
label = str2Label(label)
return self._labelDict.get(label, default)
def containsLabel(self, label):
# Allow getValue using the label string
if isinstance(label, basestring):
label = str2Label(label)
return label in self._labelDict
